The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000023.4(SGCA):c.502G>A (p.Gly168Arg)

CA8643815

498275 (ClinVar)

Gene: SGCA (HGNC:6442)
Condition: autosomal recessive limb-girdle muscular dystrophy (MONDO:0015152)
Inheritance Mode: Autosomal recessive inheritance
UUID: 6ab30f87-9161-449b-aa5c-d25719909456
Approved on: 2026-04-29
Published on: 2026-05-07

HGVS expressions

NM_000023.4:c.502G>A
NM_000023.4(SGCA):c.502G>A (p.Gly168Arg)
NC_000017.11:g.50168490G>A
CM000679.2:g.50168490G>A
NC_000017.10:g.48245851G>A
CM000679.1:g.48245851G>A
NC_000017.9:g.45600850G>A
NG_008889.1:g.7486G>A
ENST00000504073.2:c.502G>A
ENST00000511303.6:n.227G>A
ENST00000512526.2:c.493G>A
ENST00000682109.1:c.382G>A
ENST00000683226.1:n.212G>A
ENST00000683294.1:c.502G>A
ENST00000262018.8:c.502G>A
ENST00000262018.7:c.502G>A
ENST00000344627.10:c.502G>A
ENST00000502555.5:c.*161G>A
ENST00000511303.5:c.223G>A
ENST00000512526.1:c.337G>A
ENST00000513821.5:c.502G>A
ENST00000513942.5:n.293G>A
ENST00000514934.1:c.*208G>A
NM_000023.2:c.502G>A
NM_001135697.1:c.502G>A
NM_000023.3:c.502G>A
NM_001135697.2:c.502G>A
NR_135553.1:n.558G>A
NM_001135697.3:c.502G>A
NR_135553.2:n.538G>A
More

Likely Pathogenic

Met criteria codes 4
PP4 PM3 PS3_Moderate PM2_Supporting
Not Met criteria codes 2
PP3 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Limb Girdle Muscular Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SGCA Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Limb Girdle Muscular Dystrophy VCEP
The NM_000023.4: c.502G>A variant in SGCA is a missense variant predicted to cause substitution of glycine by arginine at amino acid 168, p.(Gly168Arg). This variant has been detected in at least three individuals with limb-girdle muscular dystrophy, where it was reported in unconfirmed phase with a likely pathogenic variant in two patients (c.241C>T p.(Arg81Cys), 0.25 pts, PMID: 31268554; c.246C>A p.(Ser82Arg), 0.25 pts, GRASP-LGMD Consortium internal data communication) and in unconfirmed phase with a pathogenic variant in the third patient (c.229C>T p.(Arg77Cys), 0.5 pts, PMID: 39678382) (PM3). At least one of these patients displayed progressive limb girdle muscle weakness (PP4; PMID: 39678382). The Grpmax variant allele frequency in gnomAD v4.1.1 is 0.00004605 (2/43432 East Asian alleles), which is less than the LGMD VCEP threshold for PM2_Supporting. In vitro assay in a heterologous cell system has demonstrated that this variant disrupts membrane localization of the sarcoglycan complex (PS3_Moderate, Washington University internal data). The computational predictor REVEL gives a score of 0.548, which is below the threshold of 0.7 (PP3 not met). In summary, this variant meets criteria to be classified as Likely Pathogenic for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (LGMD VCEP specifications version 2.0.0; 04/29/2026): PM3, PP4, PM2_Supporting, PS3_Moderate.
Met criteria codes
PP4
At least one patient with this variant displayed progressive limb girdle muscle weakness (PP4; PMID: 39678382).
PM3
This variant has been detected in at least three individuals with Limb-girdle muscular dystrophy, where it was reported in unconfirmed phase with a likely pathogenic variant in two patients (c.241C>T p.(Arg81Cys), 0.25 pts, PMID: 31268554; c.246C>A p.(Ser82Arg), 0.25 pts, GRASP-LGMD Consortium internal data communication) and in unconfirmed phase with a pathogenic variant in the third patient (c.229C>T p.(Arg77Cys), 0.5 pts, PMID: 39678382) (PM3). c.229C>T, c.241C>T predicted on different haplotypes; c.246C>A not present in gnomAD v2 all variant classifications independent
PS3_Moderate
In vitro assay in a heterologous cell system has demonstrated that this variant disrupts membrane localization of the sarcoglycan complex (PS3_Moderate, Washington University internal data). Concordant results across two sarcoglycan membrane localization assays: Functional score -0.85 in the WashU assay and -1.5 in Yale assay
PM2_Supporting
The Grpmax variant allele frequency in gnomAD v4.1.1 is 0.00004605 (2/43432 East Asian alleles), which is less than the LGMD VCEP threshold for PM2_Supporting. The upper bound of the 95% confidence interval for the European (non-Finnish) population also meets the criterion.
Not Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.548, which is below the threshold of 0.7 (PP3 not met). SpliceAI: 0.00
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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